Ensure output path for Slurm logs exists

Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile

MIT License

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Ensure output path for Slurm logs exists #8

Closed boulund closed 6 years ago

boulund commented 6 years ago

This PR contains two minor improvements:

Ensure the path component of the Slurm logfile arguments exists. It is a bit hacky, but at least you don't have to suffer Slurm jobs dying without any visible indication of why.
Fix the construction of the opts arguments to sbatch by converting underscores back to dashes (necessary because argparse converts all dashes (-) in command-line arguments to underscores (_)).

I hope someone finds this useful.

johanneskoester commented 6 years ago

@percyfal for me this looks ready to merge. But the slurm profile is your baby, so please let us know if you agree.

percyfal commented 6 years ago

Minor change needed when checking the output and error arguments; they are always initialized to None and os.makedirs will fail. Otherwise LGTM.

boulund commented 6 years ago

As the output and error keys always exist in arg_dict we don't need to check for their existence, but instead just check if they're set to None. Do you think it looks OK?

percyfal commented 6 years ago

Yes, you're right, let's settle for that.